Preface

Third volume and the second issue (Year 2020) of the scholarly open-access journal Translational Research in Veterinary Science (TRVS), Nicolaus Copernicus University (NCU) publishers is publishing four research papers devoted in the field of veterinary science. In this published issue of TRVS, three manuscripts based on the original research works and a case report. The first paper of Czarnik et al. (2020) published the original research paper based on the trait-associated study conducted on Polish HF cattle to find out the genetic association between bovine CXCL8 gene polymorphism and clinical mastitis and fertility trait; the second paper of Kwiatkowska et al. (2020) published the case report study on cat suffering from gastrointestinal lymphoma to examine the association of toxic encephalopathy with low dose metronidazole therapy; the third paper of Yemets (2020) published the original research paper based on the animal nutrition studies describing the dietary effects of drone larves homogenate on the homeostatic constants and the reproductive capacity of Large White gilts in Ukraine; and lastly the Bak et al. (2020) published the original research paper based on the use of algorithms for multiple DNA sequence alignment across livestock species. During this difficult period of COVID-19 pandemic year, I would like to thank all authors for their contribution to this issue. Thanks are also extended to the editorial board members, manuscripts reviewers, TRVS editorial technical staff working at NCU publisher office (Mirosława Buczyńska, Elżbieta Kossarzecka, Grzegorz Kopcewicz, and Dariusz Żulewski), who supported at every stage of the project. Most importantly, this volume of TRVS is greatly acknowledged the supported of NCU funds from newly elect JM Rector Prof. dr hab. Andrzej Sokala

Preface

Third volume and the first issue (Year 2020) of the scholarly open-access journal Translational Research in Veterinary Science (TRVS), Nicolaus Copernicus University (NCU) publishers is publishing five research papers devoted in the field of veterinary science. In this published issue of TRVS all five manuscripts based on the original research works. Olszewska- Tomczyk and Jasik (2020) published the original research paper based on the transcriptome analysis of avian pathogens; Stupar and Shostya (2020) published the original research paper based on the endocrine studies gilts affecting puberty and supplementary diets affecting reproduction in gilts; Henklewski and Spiewak (2020) published the original research paper describing etiologies and diagnostic procedures of sensory ligament injuries in Horses; Czarnik et al. (2020) published the original research paper based on the identification of two SNPs polymorphism of bovine cytokine genes in Polish HF cattle; and lastly, Bak et al. (2020) published the original research paper describing the analytical protocols of alignment mapping tools applied to the high throughput NGS data. During this difficult period of COVID-19 pandemic year, I would like to thank all authors for their contribution to this issue. Thanks are also extended to the editorial board members, manuscripts reviewers, TRVS editorial technical staff working at NCU publisher office (Mirosława Buczyńska, Elżbieta Kossarzecka, Grzegorz Kopcewicz, and Dariusz Żulewski), who supported at every stage of the project. Most importantly, this volume of TRVS is greatly acknowledged the supported of NCU funds from newly elect JM Rector Prof. dr hab. Andrzej Sokala

Preface

After the inaugural volume of a new scholarly open-access journal Translational Research in Veterinary Science (TRVS), Nicolaus Copernicus University (NCU) publishers’, we are publishing the first issue of the second volume (Year 2019) devoted in the field of veterinary science. The aim of this issue is to publish the basic researches in the field of veterinary science discipline. This second volume for the year 2019 includes five manuscripts based on the clinical research studies and next-generation genome sequencing (NGS) studies in Cattle, Pig, and Horse. Herein describe in brief, Pareek et al. (2019) have published the original research paper based on the application of NGS technology in -Omics research in cattle. Study summarized the methodological part of the NGS technology illustrating the bioinformatics tools and application of quality control (QC) to verify the quality of large set of transcriptomic (RNA-seq) data in Hereford bulls. Based on the clinical research study, Dordas-Perpinya and Bruyas (2019) paper reviewed the current status of equine embryo transfer technic in mare. Similarly, based on the clinical research study, Henklewski (2019) paper presented the comparative study between palpation and radiographic findings in Horses affected by Equine Back Disorders. Lastly, Pierzchala et al. (2019) published two original research paper based on the application of NGS technology in -Omics research in Polish Landrace pigs. In the first original research paper, Pierzchala et al. (2019a) published the RNA-seq based SNP discoveries in gluteus medius muscle transcriptome of Polish Landrace pigs, and in the second original research paper, Pierzchala et al. (2019b) published the RNA-seq based SNP discoveries in liver transcriptome of Polish Landrace pigs. For the first time, In this issue, we are publishing the genomic data of cattle (Pareek et al. 2019) and pig (Pierzchala et al. 2019a and Pierzchala et al. 2019b), respectively. These published genomics data were also published to the domesticated animal nucleotide archives web resources at the National Centre for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/sra) web site.I would like to thank all authors for their contribution. This issue would not have been possible without the great support of the editorial board members, Therefore, I would like to express our sincere thanks to all of them. I would also like to thanks to the manuscripts reviewers, TRVS editorial technical staff of NCU publisher, particularly Mirosława Buczyńska, Elżbieta Kossarzecka, and Grzegorz Kopcewicz, who supported me energetically at every stage of the project. Finally, this volume of TRVS is greatly acknowledged the supported of NCU funds from JM Rector Prof. dr hab. Andrzej Tretyn.

Preface

This inaugural volume includes five manuscripts. Four original papers based clinical and nonclinical studies in small and large domesticated animals and an invited review article are presented to the readers of TRVS. In this issue, Szczepanek et al. have reviewed the role of microRNA in domestic animals. They summarized the existing knowledge about miRNAs synthesis, mechanisms for regulation of the genome their functions in animals physiology; microRNAs as potential biomarkers for veterinary research; the implications associated with dysfunction and dysregulation. Review concludes that microRNA molecules are great targets for understanding biology, physiology and pathology in veterinary science. In the near future, these molecules may become very attractive features for their immediate implementation as biomarkers for many diseases and may contribute to enhancing global agricultural production as well. Brüssow et al. original paper analyzed the impact of unilateral ovarian removal (uni-OXV) on ovarian function, steroid hormone level, fetal distribution and development in gilts. Study concludes that by comparing to intact gilts, only long term uni-OVX could compensate ovarian development. However, short term uni-OVX affects the total number of CL and fetuses, distribution and weight of fetuses in uterine horns and steroid hormone levels. Gehrke et al. original paper reported the relations between feto-pelvic proportion and fertility of black-and-white and red-and-white Polish Holstein-Friesian cows. Study concludes that process of “Holsteinization” of domestic headache of cattle requires selection of bull’s semen not only for heifers but also older cows. Wysocka et al. original paper predicted the hepatic and pituitary gland expression of potential candidate genes in context to maintenance of oxidative balance, negative nitrogen balance, and ketosis in Polish HF and Polish Red cattle. Study conclude that understanding the genetic factors that predispose metabolic disorders in cattle would benefit the dairy industry as a whole by providing producers, breeding services, and veterinarians a tool to forecast a cow’s susceptibility to metabolic disorders. Felsmann and Felsmann original paper examined the impact of changes in Polish law on the possibility of interrupting the spread toxoplasmosis and toxocarosis. Study updated the new changes in the Polish legal acts (acts and regulations) made in recent years in context to combat toxocarosis and toxoplasmosis by the legal authorities of Polish government administration. Study concluded that state public health services do not currently possess the legal means necessary to take effective action leading to the blocking of pathways along which these zoonosis spread

Preface

In continue to the previous editions, the second volume and second issue (Year 2019) of the scholarly open-access journal Translational Research in Veterinary Science (TRVS), Nicolaus Copernicus University (NCU) publishers’ is publishing five research papers devoted in the field of veterinary science. This published issue of TRVS includes three manuscripts based on the CNVs, GWAS, veterinary public health, colibacteriosis research studies, and two short communications describing “Omics data report in brief” in cattle

Assessment of Penicillium bilaii inoculation in wheat (Triticum aestivum L.) for improving growth, yield and phosphorus availability in Mollisols of India

A field experiment was carried out with an aim to study the influence of two strains of Penicillium bilaii (PB -201 and PB-208) inoculation along with superphosphate application on growth, yield and P uptake of wheat (cv. PBW-343) and, also to examine the inoculation effect on P availability, forms of P and soil properties in Mollisols of Uttarakhand, India. The results showed that both strains of P. bilaii effectively solubilized tri-calcium phosphate in Pikovskaya agar medium, which was much higher over native fungal isolates. Wheat seed inoculation with P. bilaii strains along with superphosphate levels significantly influenced shoot height, shoot dry weight, number of total and effective tillers, yield attributes, yield components, tissue content and uptake of P. The treatment T7 (P. bilaii, strain PB-208 + 50% P) has resulted into the highest amount of shoot height (87.9 cm at 90 DAS), shoot dry weight (1.5 and 3.8 g at 60 and 90 DAS, respectively), grain (66.8 q ha-1) and straw yield (42.7 q ha-1) and P uptake (26.5 kg ha-1). The Olsen-P, organic carbon, dehydrogenase activity and fungal populations also increased in soil inoculated with P. bilaii strains combined with superphosphate application compared to the control soil. The conjoint use of the fungal strains with or, without P fertilization has developed an antagonistic interaction that has caused decline in yield, tissue content and uptake of P and its availability in soil. In conclusion, it is possible to reduce the rate of soluble P-fertilizer added by 50% without reducing yield, if wheat is inoculated with P-solubilizing fungi like P. bilaii

The role of microRNAs in animal physiology and pathology

MicroRNAs are a class of small, evolutionarily conserved, endogenous RNAs, capable of controlling gene expression. MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. They play an important regulatory role in animals at the posttranscriptional levels by targeting mRNAs for direct cleavage of mRNAs or repression of mRNA translation. The main biological function of miRNA is the post-translation regulation of cells, like: proliferation and differentiation, cell death, fat metabolism, neuronal patterning and angiogenesis.  These molecules are the main regulators of biological features of economic interest, including body growth, muscle development, signaling transduction, fat deposition, and immunology. In this review, we summarize the existing knowledge about miRNAs synthesis, mechanisms for regulation of the genome their functions in animals physiology and the implications associated with dysfunction and dysregulation

Benchmark of algorithms for multiple DNA sequence alignment across livestock species

Background: Due to the growing amount of biological data, it is often necessary to select the most optimal estimation method for DNA sequence alignment across livestock species. One of the most important benches of genomics is to modelling homology between considered DNA sequences. A multiple sequence alignment is a potent tool for molecular and evolutionary biology, and there are several programs and algorithms applicable for this purpose. The purpose of this paper was to study the most commonly used DNA alignment algorithms to select the optimal tool dedicated for short sequences.Methods: Four steps of bioinformatics pipelines were considered to benchmark the algorithms for multiple DNA sequence alignment across livestock species: 1) selection of reference genome sequences of ARS1.2 for cattle, EquCab3.0 for horse and vicPac2 for alpaca with a low E-value using TBLASTn 2) removing gaps for these sequences 3) alignment of obtained sequences using examined algorithms 4) matching the quality of aligned sequences with sequences of reference genomes by more software. The time of computation was archived for the whole analysis. The seven programs were utilized, each based on different alignment algorithms, namely: ClustalO, ClustalW, Kalign, MAFFT, MUSCLE, Probcons and T-Coffee.Results: The result obtained in this study showed that the fastest is progressive algorithms such as Kalign or MUSCLE-FAST. Moreover, the iterative algorithms like MAFFT and MUSCLE revealed a higher quality of the alignment. The T-Coffee and Probcons programs were computational cost-effective; simultaneously, they were generating a medium-quality calculation in a relatively long time. The best quality of alignment was shown by iterative variants of the MAFFT program; however, the speed of the calculations was relatively low. The fastest algorithm was Kalign, making alignment much faster than the competitors, but achieving average results in the quality of the alignment. The average speed ratio concerning the quality of the analyzed algorithms was obtained by the progressive version of MAFFT, NS1.Conclusions: We conclude that the results of this study can be used to re-alignment of variant primers in new livestock genome releases

Investigation of candidate genes for metabolic disorders expressed in liver and pituitary gland by comparing the RNA-seq data of Polish-HF and Polish-Red cattle

Background: Metabolic disorder is a major health problem in dairy cattle, particularly to high milk producing dairy cattle. It is worthily emphasized that metabolic diseases have a very complex etiology and pathogenesis, and the impact of these diseases on hepatic and pituitary gland gene expression and organism oxidative balance is not fully described. The presented study was aimed to determine and predict the hepatic and pituitary gland expression of potential candidate genes in context to maintenance of oxidative balance, negative nitrogen balance, as well as ketosis in Polish HF and Polish Red cattle.Methods: Based on the RNA-seq experimental data, we investigated the candidate genes (SOD1, SOD2, SOD3, GPx2, GPx3, GPx5, GPx6, GPx7, GPx8, BDH1, FN1, ACSL3, HMGCL, HMGCS2, BDH2, ACSL6, ACAT2, IDH3B, ACAT1, HMGCS1, ACSL4, ACSL1, PC, CPT1A, OXCT1 and ACSL5 respectively) expressions in liver and pituitary gland tissues of Polish HF and Polish Red cattle. The RNA-seq experimental design comprised of young bulls aged between 6 to 12 months were investigated. For each breed, six liver and six pituitary gland tissues were sequenced using Next-seq 500 illumina platform. The RNA-seq expression data were normalized by the reads per kilobase of exon per million reads mapped (RPKM) method.Results: By comparing the RNA-seq data of liver and pituitary gland tissues, the investigated candidate genes were highly expressed in the hepatic tissues than to pituitary gland in investigated cattle breeds. However, by comparing the Polish HF and Polish Red cattle breeds, results revealed a similar trend of gene expression profiling of all investigated candidate genes for both metabolic tissues. In case of hepatic gene expression profiling, the SOD1, FN1, HMGCL, HMGCS2, ACAT2, ACAT1, HMGCS1, ACSL1 and ACSL5 were highly expressed (FPKM values of >40), followed by SOD2, GPX3, IDH3B, PC and BDH2 as moderately expressed (FPKM values: >10 to <40), and averagely expressed SOD3, GPX5, GPX6, GPX7, GPX2, GPX8, BDH1, ACSL3, ACSL6, ACSL4, CPT1A and OXCT1 respectively, in Polish HF and Polish Red breeds. In case of pituitary gland gene expression profiling, the SOD1 and GPx3 were highly expressed (FPKM values of >40), followed by SOD2, GPX8, IDH3B, ACAT1, ACSL4 and PC as moderately expressed (FPKM values: >10 to <40), and averagely expressed SOD3, GPX3,GPX5, GPX6, GPX7, GPX2, BDH1, BDH2, ACSL3, ACSL6, CPT1A, OXCT1, FN1, HMGCL, HMGCS2, ACAT2, ACAT1, HMGCS1, ACSL1 and ACSL5 respectively, in Polish HF and Polish Red breeds.Conclusions: Based on this presented results on hepatic and pituitary gland gene expression, a further research plan is an essential pre-requisite to validate the identified candidate genes. Study indicated the understanding the genetic factors that predispose metabolic disorders in cattle would benefit the dairy industry as a whole by providing producers, breeding services, and veterinarians a tool to forecast a cow’s susceptibility to metabolic disorders

Evaluation of analytical protocols of alignment mapping tools using high throughput next-generation genome sequencing data

Background: Ever since the development of first next-generation genome sequencer (NGS) in 2005, there are rapid developments of high throughput next-generation genome sequencing (HT-NGS) techniques and tools used in genetics and genomics has become much more comfortable and cheaper. The result is the generation of a massive amount of data sets, requiring detailed analysis, which becomes impossible without the use of appropriate bioinformatics tools. One of the crucial steps in the analysis of NGS data is to map readings to a reference sequence. Although the dominance of Illumina synthesis by sequencing (SBS) technology has been noticeable in recent years, the choice of the tools is hampered and the variety of input data and reference genomes. Moreover, the tools used are crucial for result files and further analysis.Methods: The subject of this paper is the three most frequently used alignment mapping programs, which have functions to allow working with many platforms: BWA, Bowtie2 and SMALT. The task of the tested aligners is to match short sequences coming from NGS with reference sequences. The most popular: BWA and Bowtie2 use for this purpose the Burrows-Wheeler transformation and SMALT maps the sequences using hashing and dynamic programming. The presented paper aimed to compare the quality and efficiency of the alignment mapping programs under examination, due to three criteria: i) the quality of the compared sequences of different lengths and from different platforms; ii) coefficient of wrongly compared sequences; iii) the computational resources used.Results: By comparing the results of the mapping analyses for all the programs used, the least popular SMALT is the best. Obtaining the highest percentage of mapped readings for each platform and maintaining the lowest computational memory usage, turns out to be the most optimal choice.Conclusions: The results presented in this paper can be used to verify and rebuild data analysis pipelines from NGS based so far on other tools. We conclude that by using the tools under appropriate conditions, it is possible to improve the quality of the analyses, speed them up and reduce their cost